Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3127 |
| PDBID: | 6WJL |
| Chains: | HL_G |
| Organism: | Homo sapiens, Lama glama |
| Method: | XRD |
| Resolution (Å): | 3.30 |
| Reference: | 10.1016/j.xcrm.2021.100344 |
| Antibody | |
| Antibody: | D3 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Glypican-2 |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >6WJL_H|Chain B[auth F], F[auth H]|D3 Fab Heavy chain|Homo sapiens (9606) EVQLVETGGGVVKPGGSLRLSCAASGFTFSDYYMSWIRQAPGKGLEWVSYISSSGSTIYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARESGYDYVFDYWGQGTLVAVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK |
Light Chain: L
Mutation: NULL
| >6WJL_L|Chain D[auth J], H[auth L]|D3 Fab Light Chain|Homo sapiens (9606) DIQMTQSPSTLSAFVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQQLNSYPITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: G
Mutation: S35T/S72T/S135T
| >6WJL_G|Chain A[auth E], E[auth G]|Glypican-2|Homo sapiens (9606) ETGSEAKVTRSCAETRQVLGARGYSLNLIPPALITGEHLRVCPQEYTCCSSETEQRLIRETEATFRGLVEDTGSFLVHTLAARHRKFDEFFLEMLSVAQHSLTQLFSHSYGRLYAQHALIFNGLFSRLRDFYGETGEGLDDTLADFWAQLLERVFPLLHPQYSFPPDYLLCLSRLASSTDGSLQPFGDSPRRLRLQITRTLVAARAFVQGLETGRNVVSEALKVPVSEGCSQALMRLIGCPLCRGVPSLMPCQGFCLNVVRGCLSSRGLEPDWGNYLDGLLILADKLQGPFSFELTAESIGVKISEGLMYLQENSAKVSAQVFQECGPPDPVPARNRRAPPPREEAGRLWSMVTEEERPTTAAGTNLHRLVWELRERLARMRGFWARLSLTVCGDSRMAADASLEAAPCWTGAGRGRYLPPVVGGSPAEQVNNPELKVDASGPDVPTRRRRLQLRAATARMKTAALGHDLDGQGTKHHHHHH |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| H: GLU1 GLY26 PHE27 THR28 SER30 ASP31 TYR32 TYR33 TYR50 SER52 SER53 SER55 THR56 TYR58 ARG94 GLU95 SER96 GLY97 TYR98 ASP99 L: ILE2 SER26 GLN27 SER28 SER30 SER31 TRP32 TYR49 ALA50 GLN55 SER56 LEU91 ASN92 SER93 G: ASP91 THR92 PHE95 HIS98 THR99 ALA101 ALA102 ARG103 ARG105 LYS106 GLU109 THR380 THR381 ALA382 THR385 ARG389 TRP392 GLU393 GLU396 ARG397 ALA399 ARG400 PHE404 ARG407 LEU410 THR411 GLY414 ASP415 SER416 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
